Noncoastal NMDS- With Ref Piedmont Streams
R version 4.0.3 (2020-10-10) – “Bunny-Wunnies Freak Out”
Packages used for NMDS: vegan (version 2.5-7)
Methods
The document shows a series of NMDS ordinations for reference benthic communities in Virginia with environmental characteristics overlaid to evaluate natural differences in community compositions across Virginia. These NMDS will support the Genus level IBI development process. This analysis is the first run of all of reference sites and sites that were deemed reference piedmont sites in Virginia. No West Virginia DEP data is used in this analysis.Reference sites were evaluated by regional biologists.
The dataset used includes all reference stations collected in Virginia that were deemed reference through a series or water quality parameter filters and regional biologist review. If stations appeared in the dataset more than 4 times, then the most recent 4 samples were used and the rest removed. Samples that had a total number of taxa below 100 collected at the time of sampling were also removed. Taxa that occurred in the dataset <= 5% of the time were removed. The data was log10 +1 transformed. Environmental factors were compiled for each station and used to plot over the NMDS to show environmental variation associated with the community matrix. The envfit function in Vegan was used to plot the continuous environmental variables. Some environmental variables like precipitation, slope, and elevation have not been calculated for all watersheds yet and will be added at a later date.
The first step was to read in the reference site bug taxa list and environmental factors dataset for each station. Join the environmental dataset with the bug dataset to account for multiple observations of each station and collection date and time.
Check to make sure the bug and environmental join was successful:
Number of rows in Community Matrix: 783
Number or rows in Environmental Matrix: 785
The data was log10+1 transformed. Rare taxa (<=5%) were removed.
NMDS Results for Non-Coastal Streams
## Run 0 stress 0.1787787
## Run 1 stress 0.1790783
## ... Procrustes: rmse 0.002504029 max resid 0.05042826
## Run 2 stress 0.1800402
## Run 3 stress 0.1791169
## ... Procrustes: rmse 0.002979715 max resid 0.0506303
## Run 4 stress 0.1790946
## ... Procrustes: rmse 0.003184204 max resid 0.04584174
## Run 5 stress 0.1796415
## Run 6 stress 0.1794197
## Run 7 stress 0.1790037
## ... Procrustes: rmse 0.002487529 max resid 0.04534014
## Run 8 stress 0.179314
## Run 9 stress 0.178976
## ... Procrustes: rmse 0.002563227 max resid 0.04113389
## Run 10 stress 0.1789059
## ... Procrustes: rmse 0.002089364 max resid 0.04161214
## Run 11 stress 0.1870266
## Run 12 stress 0.1792536
## ... Procrustes: rmse 0.003577928 max resid 0.05002788
## Run 13 stress 0.1788356
## ... Procrustes: rmse 0.001888102 max resid 0.04268624
## Run 14 stress 0.1846527
## Run 15 stress 0.180944
## Run 16 stress 0.1789466
## ... Procrustes: rmse 0.001634449 max resid 0.04524993
## Run 17 stress 0.1809055
## Run 18 stress 0.1790442
## ... Procrustes: rmse 0.00266505 max resid 0.04579269
## Run 19 stress 0.1793592
## Run 20 stress 0.1790002
## ... Procrustes: rmse 0.002942282 max resid 0.05073364
## Run 21 stress 0.1866547
## Run 22 stress 0.1790225
## ... Procrustes: rmse 0.00298488 max resid 0.04545408
## Run 23 stress 0.1791671
## ... Procrustes: rmse 0.003386359 max resid 0.04587383
## Run 24 stress 0.1788438
## ... Procrustes: rmse 0.001474478 max resid 0.03801694
## Run 25 stress 0.1790461
## ... Procrustes: rmse 0.002782981 max resid 0.05032982
## Run 26 stress 0.1790258
## ... Procrustes: rmse 0.003040645 max resid 0.04547114
## Run 27 stress 0.1790523
## ... Procrustes: rmse 0.002707138 max resid 0.04568219
## Run 28 stress 0.1790441
## ... Procrustes: rmse 0.002661951 max resid 0.04579274
## Run 29 stress 0.1793933
## Run 30 stress 0.1790974
## ... Procrustes: rmse 0.003154143 max resid 0.04549251
## Run 31 stress 0.1810013
## Run 32 stress 0.1790062
## ... Procrustes: rmse 0.002335555 max resid 0.04532854
## Run 33 stress 0.1789101
## ... Procrustes: rmse 0.001911388 max resid 0.05045323
## Run 34 stress 0.1788858
## ... Procrustes: rmse 0.001930166 max resid 0.03760034
## Run 35 stress 0.1789635
## ... Procrustes: rmse 0.002407358 max resid 0.05052184
## Run 36 stress 0.1789768
## ... Procrustes: rmse 0.002607093 max resid 0.04162671
## Run 37 stress 0.1790041
## ... Procrustes: rmse 0.003014302 max resid 0.05080422
## Run 38 stress 0.1791678
## ... Procrustes: rmse 0.002934758 max resid 0.0500105
## Run 39 stress 0.1789644
## ... Procrustes: rmse 0.002435676 max resid 0.05055896
## Run 40 stress 0.1792212
## ... Procrustes: rmse 0.003240301 max resid 0.05010465
## Run 41 stress 0.1791985
## ... Procrustes: rmse 0.003305406 max resid 0.0498025
## Run 42 stress 0.1788399
## ... Procrustes: rmse 0.001444341 max resid 0.03847479
## Run 43 stress 0.1797901
## Run 44 stress 0.1810849
## Run 45 stress 0.1788975
## ... Procrustes: rmse 0.002097443 max resid 0.04075255
## Run 46 stress 0.1789609
## ... Procrustes: rmse 0.002398921 max resid 0.05052494
## Run 47 stress 0.1788167
## ... Procrustes: rmse 0.00153419 max resid 0.0345005
## Run 48 stress 0.179167
## ... Procrustes: rmse 0.002921762 max resid 0.05000944
## Run 49 stress 0.1797454
## Run 50 stress 0.1788138
## ... Procrustes: rmse 0.001338495 max resid 0.03340206
## Run 51 stress 0.1790042
## ... Procrustes: rmse 0.002157104 max resid 0.0452859
## Run 52 stress 0.1789642
## ... Procrustes: rmse 0.002428818 max resid 0.05054606
## Run 53 stress 0.1790493
## ... Procrustes: rmse 0.00256716 max resid 0.04542099
## Run 54 stress 0.180569
## Run 55 stress 0.1790144
## ... Procrustes: rmse 0.002950913 max resid 0.04240262
## Run 56 stress 0.179546
## Run 57 stress 0.1790032
## ... Procrustes: rmse 0.002924426 max resid 0.05071931
## Run 58 stress 0.1799167
## Run 59 stress 0.1788972
## ... Procrustes: rmse 0.002078527 max resid 0.04070022
## Run 60 stress 0.1793426
## Run 61 stress 0.1794974
## Run 62 stress 0.1868693
## Run 63 stress 0.1793748
## Run 64 stress 0.1793932
## Run 65 stress 0.178984
## ... Procrustes: rmse 0.00232877 max resid 0.0453998
## Run 66 stress 0.1806733
## Run 67 stress 0.1799345
## Run 68 stress 0.1788164
## ... Procrustes: rmse 0.001609942 max resid 0.03542758
## Run 69 stress 0.1794745
## Run 70 stress 0.1789966
## ... Procrustes: rmse 0.002265871 max resid 0.04567002
## Run 71 stress 0.1802257
## Run 72 stress 0.1790471
## ... Procrustes: rmse 0.002737429 max resid 0.05029246
## Run 73 stress 0.1802009
## Run 74 stress 0.1789141
## ... Procrustes: rmse 0.001894929 max resid 0.05046208
## Run 75 stress 0.1789612
## ... Procrustes: rmse 0.002405158 max resid 0.05053038
## Run 76 stress 0.1790018
## ... Procrustes: rmse 0.002169604 max resid 0.04532874
## Run 77 stress 0.1791345
## ... Procrustes: rmse 0.003035987 max resid 0.0506646
## Run 78 stress 0.1789539
## ... Procrustes: rmse 0.002515393 max resid 0.05065274
## Run 79 stress 0.1833642
## Run 80 stress 0.1790959
## ... Procrustes: rmse 0.003114367 max resid 0.05006005
## Run 81 stress 0.1799673
## Run 82 stress 0.1788391
## ... Procrustes: rmse 0.00157813 max resid 0.04073087
## Run 83 stress 0.1790027
## ... Procrustes: rmse 0.002924881 max resid 0.05072921
## Run 84 stress 0.1800514
## Run 85 stress 0.1789921
## ... Procrustes: rmse 0.002353372 max resid 0.05019188
## Run 86 stress 0.1790622
## ... Procrustes: rmse 0.003385237 max resid 0.05096852
## Run 87 stress 0.1794752
## Run 88 stress 0.1792028
## ... Procrustes: rmse 0.00332282 max resid 0.04974752
## Run 89 stress 0.178955
## ... Procrustes: rmse 0.00252075 max resid 0.05067149
## Run 90 stress 0.1789136
## ... Procrustes: rmse 0.001882456 max resid 0.05044315
## Run 91 stress 0.1800532
## Run 92 stress 0.1799545
## Run 93 stress 0.1790093
## ... Procrustes: rmse 0.002213583 max resid 0.04533748
## Run 94 stress 0.1797498
## Run 95 stress 0.1790201
## ... Procrustes: rmse 0.002997493 max resid 0.04546739
## Run 96 stress 0.1791602
## ... Procrustes: rmse 0.003373377 max resid 0.05073323
## Run 97 stress 0.1797267
## Run 98 stress 0.1790374
## ... Procrustes: rmse 0.003197673 max resid 0.0509233
## Run 99 stress 0.1800704
## Run 100 stress 0.1790026
## ... Procrustes: rmse 0.002303792 max resid 0.04573901
## Run 101 stress 0.1789469
## ... Procrustes: rmse 0.001639198 max resid 0.04524654
## Run 102 stress 0.1793303
## Run 103 stress 0.1791304
## ... Procrustes: rmse 0.002928179 max resid 0.05054952
## Run 104 stress 0.1791309
## ... Procrustes: rmse 0.003002259 max resid 0.05063083
## Run 105 stress 0.179005
## ... Procrustes: rmse 0.00218341 max resid 0.04529602
## Run 106 stress 0.1791979
## ... Procrustes: rmse 0.003283326 max resid 0.04983816
## Run 107 stress 0.1806952
## Run 108 stress 0.1788983
## ... Procrustes: rmse 0.002111765 max resid 0.04074243
## Run 109 stress 0.179694
## Run 110 stress 0.1810268
## Run 111 stress 0.1791611
## ... Procrustes: rmse 0.00345752 max resid 0.05080635
## Run 112 stress 0.1834986
## Run 113 stress 0.1792974
## Run 114 stress 0.1791131
## ... Procrustes: rmse 0.003026405 max resid 0.05066145
## Run 115 stress 0.1789099
## ... Procrustes: rmse 0.001898634 max resid 0.05043461
## Run 116 stress 0.1789104
## ... Procrustes: rmse 0.001921786 max resid 0.05046668
## Run 117 stress 0.1795866
## Run 118 stress 0.1820863
## Run 119 stress 0.1799267
## Run 120 stress 0.1794766
## Run 121 stress 0.1788353
## ... Procrustes: rmse 0.001882728 max resid 0.04270471
## Run 122 stress 0.1793657
## Run 123 stress 0.1790809
## ... Procrustes: rmse 0.002485292 max resid 0.05044364
## Run 124 stress 0.1793388
## Run 125 stress 0.1789624
## ... Procrustes: rmse 0.002379664 max resid 0.05051404
## Run 126 stress 0.1818149
## Run 127 stress 0.179439
## Run 128 stress 0.178884
## ... Procrustes: rmse 0.001988346 max resid 0.0404745
## Run 129 stress 0.1815045
## Run 130 stress 0.1796759
## Run 131 stress 0.1797622
## Run 132 stress 0.1788563
## ... Procrustes: rmse 0.002466209 max resid 0.04311143
## Run 133 stress 0.1788858
## ... Procrustes: rmse 0.001962609 max resid 0.03725129
## Run 134 stress 0.1818615
## Run 135 stress 0.17944
## Run 136 stress 0.181253
## Run 137 stress 0.1789997
## ... Procrustes: rmse 0.00292363 max resid 0.05071451
## Run 138 stress 0.1795222
## Run 139 stress 0.1800116
## Run 140 stress 0.1792009
## ... Procrustes: rmse 0.003273409 max resid 0.04981916
## Run 141 stress 0.1871008
## Run 142 stress 0.179262
## ... Procrustes: rmse 0.003228282 max resid 0.05091956
## Run 143 stress 0.1805659
## Run 144 stress 0.1791994
## ... Procrustes: rmse 0.003329148 max resid 0.04976324
## Run 145 stress 0.1795558
## Run 146 stress 0.186486
## Run 147 stress 0.1797707
## Run 148 stress 0.1855824
## Run 149 stress 0.178953
## ... Procrustes: rmse 0.002463701 max resid 0.05059836
## Run 150 stress 0.1850121
## Run 151 stress 0.1789631
## ... Procrustes: rmse 0.002379757 max resid 0.05049656
## Run 152 stress 0.179668
## Run 153 stress 0.1788292
## ... Procrustes: rmse 0.001874587 max resid 0.03740593
## Run 154 stress 0.1791609
## ... Procrustes: rmse 0.003380909 max resid 0.05073613
## Run 155 stress 0.1861242
## Run 156 stress 0.1794818
## Run 157 stress 0.1797745
## Run 158 stress 0.1791128
## ... Procrustes: rmse 0.003014708 max resid 0.05064558
## Run 159 stress 0.1792149
## ... Procrustes: rmse 0.003888058 max resid 0.05109601
## Run 160 stress 0.1790411
## ... Procrustes: rmse 0.002625705 max resid 0.04578362
## Run 161 stress 0.179157
## ... Procrustes: rmse 0.003361845 max resid 0.05071439
## Run 162 stress 0.1787763
## ... New best solution
## ... Procrustes: rmse 0.0003581806 max resid 0.0085787
## ... Similar to previous best
## *** Solution reached##
## Call:
## metaMDS(comm = NoncoastalFive[, 6:108], k = 3, trymax = 1000)
##
## global Multidimensional Scaling using monoMDS
##
## Data: NoncoastalFive[, 6:108]
## Distance: bray
##
## Dimensions: 3
## Stress: 0.1787763
## Stress type 1, weak ties
## Two convergent solutions found after 162 tries
## Scaling: centring, PC rotation, halfchange scaling
## Species: expanded scores based on 'NoncoastalFive[, 6:108]'
## NMDS1 NMDS2 r2 Pr(>r)
## Year 0.99272 0.12042 0.0160 0.21
## JulianDate -0.40251 0.91542 0.7186 0.01 **
## Latitude -0.54298 -0.83975 0.0221 0.10 .
## Longitude -0.63370 -0.77358 0.0267 0.06 .
## totalArea_sqMile -0.77223 -0.63534 0.3317 0.01 **
## ELEVMEAN 0.92445 0.38130 0.2053 0.01 **
## SLPMEAN 0.89201 0.45201 0.1469 0.01 **
## wshdRain_mmyr -0.76226 -0.64727 0.3131 0.01 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 99Plot with Stations: Non-Coastal
Season: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:108], grouping = samplescoresenv_noncoast$Season, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Fall Spring
## delta 0.6362 0.6316
## n 396 387
##
## Chance corrected within-group agreement A: 0.046
## Based on observed delta 0.6339 and expected delta 0.6645
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Reference Type: Re-Pied or Ref
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:108], grouping = samplescoresenv_noncoast$X, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Ref Ref-Pied
## delta 0.6547 0.6492
## n 684 99
##
## Chance corrected within-group agreement A: 0.01578
## Based on observed delta 0.654 and expected delta 0.6645
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Ecoregion: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:108], grouping = samplescoresenv_noncoast$US_L3NAME, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Blue Ridge Central Appalachians Northern Piedmont Piedmont
## delta 0.5946 0.6055 0.6492 0.6329
## n 154 40 124 213
## Ridge and Valley
## delta 0.6573
## n 252
##
## Chance corrected within-group agreement A: 0.04529
## Based on observed delta 0.6344 and expected delta 0.6645
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Basin: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:108], grouping = samplescoresenv_noncoast$Basin_Code, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Appomattox Chowan-Dismal James-Middle James-Upper New Potomac-Lower
## delta 0.5805 0.584 0.6296 0.6532 0.6506 0.6493
## n 18 24 81 114 78 40
## Potomac-Shenandoah Rappahannock Roanoke Tennessee-Big Sandy
## delta 0.6553 0.6397 0.62 0.6036
## n 41 128 101 16
## Tennessee-Clinch Tennessee-Holston Yadkin York
## delta 0.6268 0.6257 0.5709 0.6224
## n 50 53 4 35
##
## Chance corrected within-group agreement A: 0.04623
## Based on observed delta 0.6338 and expected delta 0.6645
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Admin Region: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:108], grouping = samplescoresenv_noncoast$ASSESS_REG, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## BRRO NRO PRO SWRO VRO
## delta 0.646 0.6644 0.619 0.6334 0.6481
## n 258 197 55 156 117
##
## Chance corrected within-group agreement A: 0.02704
## Based on observed delta 0.6465 and expected delta 0.6645
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999##Bioregion: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:108], grouping = samplescoresenv_noncoast$Bioregion, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Mountain Piedmont
## delta 0.6473 0.6493
## n 446 337
##
## Chance corrected within-group agreement A: 0.02454
## Based on observed delta 0.6482 and expected delta 0.6645
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Sample Method: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:108], grouping = samplescoresenv_noncoast$Gradient, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## MACS Riffle
## delta 0.6094 0.6587
## n 39 744
##
## Chance corrected within-group agreement A: 0.01239
## Based on observed delta 0.6563 and expected delta 0.6645
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Stream Order: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:108], grouping = samplescoresenv_noncoast$Order, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## 1 2 3 4 5
## delta 0.6367 0.6589 0.6305 0.6119 0.5699
## n 266 216 165 103 33
##
## Chance corrected within-group agreement A: 0.04378
## Based on observed delta 0.6354 and expected delta 0.6645
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Stream Order Categories: Non-coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:108], grouping = samplescoresenv_noncoast$StreamCate, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Large Medium Small
## delta 0.6043 0.6305 0.6536
## n 136 165 482
##
## Chance corrected within-group agreement A: 0.03665
## Based on observed delta 0.6401 and expected delta 0.6645
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Water Quality Standard Class: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:108], grouping = samplescoresenv_noncoast$WQS_CLASS, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## III IV V VI
## delta 0.6513 0.6448 0.6313 0.6012
## n 309 184 87 203
##
## Chance corrected within-group agreement A: 0.04507
## Based on observed delta 0.6346 and expected delta 0.6645
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Natural Trout Water WQS: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:108], grouping = samplescoresenv_noncoast$WQS_TROUT, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Yes
## delta 0.6598 0.6221
## n 493 290
##
## Chance corrected within-group agreement A: 0.02808
## Based on observed delta 0.6458 and expected delta 0.6645
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999#Ecoregion separated by Season
Bioregion and Season
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:108], grouping = samplescoresenv_noncoast$BioregionSeason, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## MountainFall MountainSpring PiedmontFall PiedmontSpring
## delta 0.6234 0.6052 0.6091 0.6241
## n 225 221 171 166
##
## Chance corrected within-group agreement A: 0.07403
## Based on observed delta 0.6153 and expected delta 0.6645
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Bioregion, Stream Size and Season: Non-coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:108], grouping = samplescoresenv_noncoast$Bioregionsize, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## LargeMountainFall LargeMountainSpring LargePiedmontFall
## delta 0.4825 0.5487 0.573
## n 29 27 42
## LargePiedmontSpring MediumMountainFall MediumMountainSpring
## delta 0.588 0.5731 0.5653
## n 38 51 50
## MediumPiedmontFall MediumPiedmontSpring SmallMountainFall
## delta 0.5818 0.5952 0.6105
## n 32 32 145
## SmallMountainSpring SmallPiedmontFall SmallPiedmontSpring
## delta 0.5768 0.5983 0.6072
## n 144 97 96
##
## Chance corrected within-group agreement A: 0.1192
## Based on observed delta 0.5853 and expected delta 0.6645
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999#Bioregion separated by Season
